So my advice is - backup all your data & get a new drive if you find even
one bad sector with scandisk.

If on other hand scandisk in thorough/surface scans doesn't show any bad sectors & you just face this question each time windows starts it maybe either a trojan/malware that marked a cluster as bad, but scandisk normally does not test bad clusters, so it comes out as clean unless you enable registry to test bad clusters (MSKB Q127055 ).

Or maybe a copy protection scheme has marked a sector as bad on hard
disk(yes some programs do that).